[willwashburn]

Summary

pnpm audit --prod reported 16 vulnerabilities (1 critical, 4 high, 11 moderate), all transitive. After this change: 0 known vulnerabilities.

• Bump @daytonaio/sdk ^0.179.0 → ^0.185.0 in packages/deploy and packages/daytona-runner (dev + peer). The SDK is the path to the critical shell-quote advisory and the four high protobufjs advisories — in the package that executes sandbox commands.
• Add pnpm.overrides in the root manifest for what the SDK bump alone didn't fix:
  • shell-quote: >=1.8.4 — critical, shell injection via unescaped newlines
  • @opentelemetry/otlp-transformer>protobufjs: >=8.2.0 and @grpc/proto-loader>protobufjs: >=7.5.8 <8.0.0 — path-specific because the tree has two protobufjs lineages; a flat >=8.2.0 would break @grpc/proto-loader (requires ^7.5.5)
  • hono: >=4.12.21, qs: >=6.15.2 — moderates via @modelcontextprotocol/sdk
  • ws: >=8.20.1, plus a pnpm.packageExtensions entry making ws a direct dep of @daytonaio/sdk — overrides don't apply to peer-only deps (it reaches the tree solely via isomorphic-ws)
• Align @relayfile/adapter-core at ^0.3.31 in @agentworkforce/runtime to match persona-kit (was ^0.3.29).

Verification

• pnpm audit --prod → No known vulnerabilities found
• pnpm -r build && pnpm typecheck && pnpm test → all green (no source changes; manifests + lockfile only)
• pnpm why @daytonaio/sdk -r → 0.185.0 resolved everywhere; ws resolves to 8.21.0

Maintenance

Each override is tech debt to remove once the owning dependency (@daytonaio/sdk, @modelcontextprotocol/sdk) ships a release that no longer pulls the vulnerable range. The packageExtensions entry for ws should be removed together with the ws override.

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💡 Codex Review

workforce/package.json

Line 10 in bc9bcab

"@opentelemetry/otlp-transformer>protobufjs": ">=8.2.0",

Keep legacy OTLP transformer on protobufjs 7

This override applies to both OTLP transformer lineages in the lockfile, including the production path packages/runtime → @agent-relay/events → @opentelemetry/exporter-trace-otlp-http@0.207.0 → @opentelemetry/otlp-transformer@0.207.0; that transformer declares protobufjs: ^7.3.0, but the lock now forces it to 8.6.2. In environments that enable the trace exporter from @agent-relay/events, this runs the older transformer against an unsupported major version, so the override should be version-qualified (keep 0.207.x on a patched 7.x such as >=7.5.8 <8, while only the 0.217.x lineage is forced to patched 8.x).

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No actionable comments were generated in the recent review. 🎉

ℹ️ Recent review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro Plus

Run ID: a4f71cf6-dd5d-461e-b37e-13780d26d270

📥 Commits

Reviewing files that changed from the base of the PR and between e0e9e86 and cd226b2.

⛔ Files ignored due to path filters (1)

• pnpm-lock.yaml is excluded by !**/pnpm-lock.yaml

📒 Files selected for processing (4)

• package.json
• packages/daytona-runner/package.json
• packages/deploy/package.json
• packages/runtime/package.json

---

📝 Walkthrough

Walkthrough

This pull request updates dependencies across the workspace. The root package.json configures pnpm dependency resolution overrides to address compatibility constraints for protobufjs and other transitive dependencies. Multiple packages then upgrade @daytonaio/sdk to version 0.185.0, and the runtime package upgrades @relayfile/adapter-core to 0.3.31.

Changes

Dependency Updates

Layer / File(s)	Summary
Root pnpm dependency resolution configuration package.json	Adds pnpm overrides for shell-quote, @opentelemetry/otlp-transformer, @grpc/proto-loader with protobufjs version constraints, and minimum versions for hono, ws, and qs. Extends @daytonaio/sdk@* with a compatible ws dependency declaration.
@daytonaio/sdk version upgrades across packages packages/daytona-runner/package.json, packages/deploy/package.json	Updates @daytonaio/sdk from ^0.179.0 to ^0.185.0 in both peerDependencies and devDependencies of daytona-runner, and in dependencies of deploy.
Runtime adapter-core dependency upgrade packages/runtime/package.json	Bumps @relayfile/adapter-core from ^0.3.29 to ^0.3.31.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~8 minutes

Poem

🐰 Dependenc-hop hop, all versions aligned,
SDK bumped, no conflicts to mind,
Overrides and extensions, a tidy array,
Package trees harmonize, hip hip hooray! 🌳✨

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title clearly summarizes the main change: fixing vulnerable transitive dependencies and aligning adapter-core versions, which directly matches the changeset.
Description check	✅ Passed	The description comprehensively covers the changeset, explaining the vulnerabilities fixed, specific dependency bumps, pnpm configuration changes, verification steps, and maintenance notes.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.

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✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch advisor/001-dependency-vulnerability-remediation

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[willwashburn]

Good catch — confirmed and fixed in cd226b2.

Verified the defect first: the lockfile's @opentelemetry/otlp-transformer@0.207.0 snapshot (reached via packages/runtime → @agent-relay/events → @opentelemetry/exporter-trace-otlp-http@0.207.0) was resolving protobufjs: 8.6.2 against its declared ^7.3.0, exactly as described.

The single un-qualified override is now split into two version-qualified entries:

"@opentelemetry/otlp-transformer@<0.217.0>protobufjs": ">=7.5.8 <8.0.0",
"@opentelemetry/otlp-transformer@>=0.217.0>protobufjs": ">=8.2.0",

Post-fix lockfile resolutions:

• otlp-transformer@0.207.0 → protobufjs 7.6.3 (patched 7.x line, satisfies the advisories)
• otlp-transformer@0.217.0 → protobufjs 8.6.2
• @grpc/proto-loader paths unchanged on 7.6.3 (covered by its own pre-existing override)

pnpm audit --prod still reports no known vulnerabilities, and the full pnpm -r build && pnpm typecheck && pnpm test gate passes (880 tests, 0 failures).